BioJava is a project dedicated to providing Java tools for processing biological data.
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Category: Scientific
bedtools – powerful toolset for genome arithmetic
The bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks.
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EMBOSS – software analysis package for molecular biology
EMBOSS is The European Molecular Biology Open Software Suite developed for the needs of the molecular biology (e.g. EMBnet) user community.
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Clustal Omega – multiple sequence alignment program
Clustal Omega is a multiple sequence alignment program for protein and DNA/RNA using seeded guide trees and HMM profile-profile techniques.
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Basic Local Alignment Search Tool – find regions of similarity between biological sequences
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
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Taverna Workbench – tools for designing and executing workflow
The Taverna workbench is an open source software tool for designing and executing bioinformatics workflows created by the myGrid project.
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geWorkbench – software platform for integrated genomic data analysis
geWorkbench (genomics Workbench) is a Java-based open-source platform for integrated genomics.
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Bioclipse – workbench for the life sciences
The Bioclipse project is a visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP).
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8 Essential Free and Open Source Python Maths Tools
Great libraries and tools that are ideal for mathematicians working with Python.
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statsmodels – statistical modeling and econometrics in Python
statsmodels is a Python package that provides a complement to SciPy for statistical computations.
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mpmath – Python library for arbitrary-precision floating-point arithmetic
mpmath is a Python library for arbitrary-precision floating-point arithmetic.
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ADiPy – automatic differentiation library
ADiPy is an open source Python automatic differentiation library. It’s a simple tool for handling arbitrary order automatic differentiation.
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patsy – Python package for statistical data transformations
patsy is a Python library for describing statistical models (especially linear models) and building design matrices.
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tidytext – text mining using dplyr, ggplot2, and other tidy tools
tidytext is text mining for word processing and sentiment analysis using ‘dplyr’, ‘ggplot2’, and other tidy tools.
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quanteda – R package for Quantitative Analysis of Textual Data
quanteda (Quantitative Analysis of Textual Data) is an R package for managing and analyzing text.
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wordcloud – create attractive word clouds, visualize differences and similarity between documents
wordcloud creates attractive word clouds, visualize differences and similarity between documents, and avoid over-plotting in scatter plots.
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tm – Text Mining Infrastructure in R
tm (shorthand for Text Mining Infrastructure in R) provides a framework for text mining applications within R.
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stringi – fast and portable character string processing in R
stringi is an R package for fast, portable, correct, consistent, and convenient string/text processing in any locale or character encoding.
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stringr – string manipulation in R
The stringr package provides a cohesive set of functions designed to make working with strings as easy as possible.
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UDPipe – R package for Tokenization, Tagging, Lemmatization and Dependency Parsing
UDPipe provides language-agnostic tokenization, tagging, lemmatization and dependency parsing of raw text.
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